Genetic variability is a major feature of the human immunodeficiency virus type 1 HIV-1 and considered the key factor to frustrating efforts to halt the virus epidemic. In this study, we aimed to investigate the genetic variability of HIV-1 strains among children and adolescents born from 1992 to 2009 in the state of Sao Paulo, Brazil.

Methodology

Plasma and peripheral blood mononuclear cells PBMC were collected from 51 HIV-1-positive children and adolescents on ART followed between September 1992 and July 2009. After extraction, the genetic materials were used in a polymerase chain reaction PCR to amplify the viral near full length genomes NFLGs from 5 overlapped fragments. NFLGs and partial amplicons were directly sequenced and data were phylogenetically inferred.

Results

Of the 51 samples studied, the NFLGs and partial fragments of HIV-1 from 42 PBMCs and 25 plasma were successfully subtyped. Results based on proviral DNA revealed that 22 52.4% patients were infected with subtype B, 16 38.1% were infected with BF1 mosaic variants and 4 9.5% were infected with sub-subtype F1. All the BF1 recombinants were unique and distinct from any previously identified unique or circulating recombinant forms in South America. Evidence of dual infections was detected in 3 patients coinfected with the same or distinct HIV-1 subtypes. Ten of the 31 32.2% and 12 of the 21 57.1% subjects with recovered proviral and plasma, respectively, protease sequences were infected with major mutants resistant to protease inhibitors. The V3 sequences of 14 patients with available sequences from PBMC-or plasma were predicted to be R5-tropic virus except for two patients who harbored an X4 strain.

Conclusions

The high proportion of HIV-1 BF1 recombinant, coinfection rate and vertical transmission in Brazil merits urgent attention and effective measures to reduce the transmission of HIV among spouses and sex partners.